TABLE 1.
Drug-DNA structures examined with knowledge-based energy functions
| NBD_ID* | DNA sequence | Drug composition† |
|---|---|---|
| 2:1 Drug-DNA complexes | ||
| bdd002 | CCAGTACTGG | ImHpPyPy-β-Dp |
| bdd003 | CCAGTACTGG | ImPyPyPy-β-Dp |
| gdj057 | CCAGGCCTGG | ImImPyPy-β-Dp |
| dd0020 | CCAGATCTGG | ImPyHpPy-β-Dp |
| dd0021 | CCAGATCTGG | ImPyPyPy-β-Dp |
| gdh060 | GTATATAC | PyPyPy (distamycin) |
| gdj054 | CATGGCCATG | ImIm (di-imidazole lexitropsin) |
| 1:1 Drug-DNA complexes | ||
| dd0014 | CGCATATTTGCG | PlBiBiBiBz (tri-benzimidazole) |
| gd1003 | CGCAAATTTGCG | PyPyPy (distamycin) |
| gd1004 | CGCGATATCGCG | PyPy (netropsin) |
| gd1008 | CGCGAATTCGCG | IdBz (DAPI) |
| gd1018 | CGCGAATTCGCG | PyPy (netropsin) |
| gd1030 | CGCGTTAACGCG | PyPy (netropsin) |
| gd1033 | CGCGAATTCGCG | PiBiBiBz (benzimidazole derivative) |
| gd1038 | CGCGAATTCGCG | ImPy (imidazole-pyrrole lexitropsin) |
| gd1039 | CGCAAATTTGCG | PlBiBiBiBz (tri-benzimidazole) |
| gd1047 | CGCGAATTCGCG | PrBiBiBz (Hoescht 33258) |
| gd1052 | CGCGAATTCGCG | BiBiBz (Hoescht 33258 analog) |
| Drug-nucleosomal DNA complexes | ||
| pd0328 | …AGTGTA… | ImPyImPy-γ-PyPyPyPy-β-Dp |
| pd0329 | …CGTGTT…, …GTGTAT… | ImPyPyPy-γ-PyPyPyPy-β-Dp |
| …AGTTTC…, …GGAATT… | ||
| pd0330 | …AGGATA… | ImImPyPy-γ-PyPyPyPy-β-Dp |
*
NDB_ID refers to the identification code of the complex in the Nucleic Acid Database (Berman et al., 1992).
†
The following abbreviations are used for drug subunits: Im, imidazole; Py, pyrrole; Hp, hydroxypyrrole; Pr, piperazine; Bz, benzene; Pl, pyrrolidine; Bi, benzimidazole; Id, indole. The β in the chemical formulae refers to a β-alanine that follows the sequence of peptide-linked subunits in the polyamide ligands and the Dp to the 3-amino-(dimethylpropylamine) group at the tail of these molecules. The γ refers to a γ-aminobutyric acid hairpin turn used to link pairs of polyamide chains bound to nucleosomal DNA.